Mercurial > repos > tduigou > seq_to_db
diff output.json @ 1:5db1c2b9edb8 draft
planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools commit fa4c85dd6ad48d404a28e21667f18b628bbdc702-dirty
| author | tduigou |
|---|---|
| date | Fri, 11 Jul 2025 14:16:33 +0000 |
| parents | 178d068648f4 |
| children | d77ff06f5dc9 |
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--- a/output.json Thu Jun 12 08:27:18 2025 +0000 +++ b/output.json Fri Jul 11 14:16:33 2025 +0000 @@ -1,65 +1,78 @@ { "summary": { "num_errors": 0, - "num_failures": 3, + "num_failures": 1, "num_skips": 0, - "num_tests": 4 + "num_tests": 2 }, "tests": [ { "data": { "inputs": { - "adv|execution_enable": false, - "annotation_column": "annotation", - "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", - "fragment_column": "fragment", "genbank_files": { - "id": "d1dc40ebed860870", + "id": "5035e3bab9835d6e", "src": "hdca" }, - "sequence_column": "sequence", - "table": "sample" + "json_generating": false, + "json_use|json_conf": { + "id": "48861e2bb98fa8f3", + "src": "hda" + }, + "json_use|use_json_paramers": true }, "job": { - "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmphs5lamwi/files/8/6/d/dataset_86d5129f-932a-4577-895e-245fe4d628fc.dat,/tmp/tmphs5lamwi/files/5/d/a/dataset_5dae2e32-d3f9-4f9b-9732-e6e2d297c2a7.dat,/tmp/tmphs5lamwi/files/0/9/a/dataset_09a835e8-673b-43e3-9bb3-f51c3a727f59.dat,/tmp/tmphs5lamwi/files/3/3/7/dataset_337d084d-9ace-4611-ac83-5ad372068c7f.dat,/tmp/tmphs5lamwi/files/6/f/2/dataset_6f2d701c-7b19-4604-a1ee-a74bd2a57870.dat' --sequence_column 'sequence' --annotation_column 'annotation' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --output '/tmp/tmphs5lamwi/job_working_directory/000/6/outputs/dataset_18f1dadc-56f5-4df2-beeb-04c270bb1b29.dat' --file_name_mapping '/tmp/tmphs5lamwi/files/8/6/d/dataset_86d5129f-932a-4577-895e-245fe4d628fc.dat:p7_L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/5/d/a/dataset_5dae2e32-d3f9-4f9b-9732-e6e2d297c2a7.dat:p6_Nt-IgKLsequence.gb,/tmp/tmphs5lamwi/files/0/9/a/dataset_09a835e8-673b-43e3-9bb3-f51c3a727f59.dat:p6_Kozak-ATG.gb,/tmp/tmphs5lamwi/files/3/3/7/dataset_337d084d-9ace-4611-ac83-5ad372068c7f.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/6/f/2/dataset_6f2d701c-7b19-4604-a1ee-a74bd2a57870.dat:HC_Amp_ccdB.gb' --json_conf 'None' --execution_enable 'false'", + "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmp_qydb9xn/files/8/c/6/dataset_8c6c4607-b545-411e-8565-3c6ca3472443.dat,/tmp/tmp_qydb9xn/files/e/b/6/dataset_eb604a05-357c-45df-ae5a-81ddb65244e3.dat,/tmp/tmp_qydb9xn/files/3/6/6/dataset_366741cf-94b2-42de-8d64-7f00e58563e0.dat,/tmp/tmp_qydb9xn/files/f/f/1/dataset_ff11bb17-ed2d-415e-96cf-e5ed35c7d997.dat,/tmp/tmp_qydb9xn/files/5/8/6/dataset_5861c673-e009-436c-9020-a23df5356851.dat' --use_json_paramers 'true' --json_conf '/tmp/tmp_qydb9xn/files/8/c/a/dataset_8ca49aab-9732-422b-bd76-9975c97f5f2a.dat' --output '/tmp/tmp_qydb9xn/job_working_directory/000/7/outputs/dataset_b5f885e2-68c2-4441-9ade-922799b2cfd6.dat' --file_name_mapping '/tmp/tmp_qydb9xn/files/8/c/6/dataset_8c6c4607-b545-411e-8565-3c6ca3472443.dat:p7_L7Ae-Weiss.gb,/tmp/tmp_qydb9xn/files/e/b/6/dataset_eb604a05-357c-45df-ae5a-81ddb65244e3.dat:p6_Nt-IgKLsequence.gb,/tmp/tmp_qydb9xn/files/3/6/6/dataset_366741cf-94b2-42de-8d64-7f00e58563e0.dat:p6_Kozak-ATG.gb,/tmp/tmp_qydb9xn/files/f/f/1/dataset_ff11bb17-ed2d-415e-96cf-e5ed35c7d997.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmp_qydb9xn/files/5/8/6/dataset_5861c673-e009-436c-9020-a23df5356851.dat:HC_Amp_ccdB.gb' --json_generating 'false' --json_output 'XXXX' && echo \"DEBUG\" && cat \"XXXX\"", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-06-12T08:11:40.445752", + "create_time": "2025-07-11T14:13:47.541606", "dependencies": [], - "exit_code": 0, - "external_id": "126337", - "galaxy_version": "24.2", + "exit_code": 1, + "external_id": "133184", + "galaxy_version": "25.0", "handler": null, - "history_id": "d1dc40ebed860870", - "id": "9b05862cf50a24d4", + "history_id": "5035e3bab9835d6e", + "id": "cf8d16af14dc294f", "inputs": { "genbank_files1": { - "id": "d1dc40ebed860870", + "id": "5035e3bab9835d6e", "src": "hda", - "uuid": "86d5129f-932a-4577-895e-245fe4d628fc" + "uuid": "8c6c4607-b545-411e-8565-3c6ca3472443" }, "genbank_files2": { - "id": "8a8d0bbb0c3dafa4", + "id": "6a141869249298e9", "src": "hda", - "uuid": "5dae2e32-d3f9-4f9b-9732-e6e2d297c2a7" + "uuid": "eb604a05-357c-45df-ae5a-81ddb65244e3" }, "genbank_files3": { - "id": "bf0fa404613c4f02", + "id": "8ca00df555c44d56", "src": "hda", - "uuid": "09a835e8-673b-43e3-9bb3-f51c3a727f59" + "uuid": "366741cf-94b2-42de-8d64-7f00e58563e0" }, "genbank_files4": { - "id": "f71740853e0eea8f", + "id": "be795001aeb7b4a0", "src": "hda", - "uuid": "337d084d-9ace-4611-ac83-5ad372068c7f" + "uuid": "ff11bb17-ed2d-415e-96cf-e5ed35c7d997" }, "genbank_files5": { - "id": "5f099fbe1e7e1218", + "id": "8fbddce2c6d1629d", "src": "hda", - "uuid": "6f2d701c-7b19-4604-a1ee-a74bd2a57870" + "uuid": "5861c673-e009-436c-9020-a23df5356851" + }, + "json_use|json_conf": { + "id": "48861e2bb98fa8f3", + "src": "hda", + "uuid": "8ca49aab-9732-422b-bd76-9975c97f5f2a" } }, - "job_messages": [], + "job_messages": [ + { + "code_desc": "", + "desc": "Fatal error: Exit code 1 ()", + "error_level": 3.0, + "exit_code": 1, + "type": "exit_code" + } + ], "job_metrics": [], "job_runner_name": null, "job_stderr": "", @@ -68,62 +81,62 @@ "output_collections": {}, "outputs": { "output": { - "id": "9b05862cf50a24d4", + "id": "cf8d16af14dc294f", "src": "hda", - "uuid": "18f1dadc-56f5-4df2-beeb-04c270bb1b29" + "uuid": "b5f885e2-68c2-4441-9ade-922799b2cfd6" } }, "params": { "__input_ext": "\"input\"", - "adv": "{\"execution_enable\": false, \"json_conf\": null}", - "annotation_column": "\"annotation\"", - "chromInfo": "\"/tmp/tmphs5lamwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", - "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"", + "chromInfo": "\"/tmp/tmp_qydb9xn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", - "fragment_column": "\"fragment\"", "genbank_files": "{\"values\": [{\"id\": 1, \"src\": \"hdca\"}]}", - "sequence_column": "\"sequence\"", - "table": "\"sample\"" + "json_generating": "false", + "json_use": "{\"__current_case__\": 1, \"json_conf\": {\"values\": [{\"id\": 6, \"src\": \"hda\"}]}, \"use_json_paramers\": true}" }, - "state": "ok", - "stderr": "", - "stdout": "Execution disabled because sequence_column is set to 'false'.\n", + "state": "error", + "stderr": "cat: XXXX: No such file or directory\n", + "stdout": "Execution blocked by config (execution = false)\nDEBUG\n", "tool_id": "seq_to_db", - "tool_stderr": "", - "tool_stdout": "Execution disabled because sequence_column is set to 'false'.\n", - "update_time": "2025-06-12T08:11:46.862307", + "tool_stderr": "cat: XXXX: No such file or directory\n", + "tool_stdout": "Execution blocked by config (execution = false)\nDEBUG\n", + "update_time": "2025-07-11T14:13:54.198241", "user_email": "planemo@galaxyproject.org", - "user_id": "d1dc40ebed860870" + "user_id": "5035e3bab9835d6e" }, "output_problems": [ - "Output output: different than expected\nExpected 5+-0 lines in the output found 0" + "Job in error state.. tool_id: seq_to_db, exit_code: 1, stderr: cat: XXXX: No such file or directory\n.", + "Job in error state.. tool_id: seq_to_db, exit_code: 1, stderr: cat: XXXX: No such file or directory\n." ], "status": "failure", - "test_index": 0, - "time_seconds": 26.20578122138977, + "test_index": 1, + "time_seconds": 28.040581941604614, "tool_id": "seq_to_db", - "tool_version": "0.1.0+galaxy0" + "tool_version": "0.2.0+galaxy1" }, "has_data": true, - "id": "seq_to_db-0" + "id": "seq_to_db-1" }, { "data": { "inputs": { - "adv|json_conf": { - "id": "faf36c8bb3bbf1fc", - "src": "hda" + "genbank_files": { + "id": "6a141869249298e9", + "src": "hdca" }, - "genbank_files": { - "id": "8a8d0bbb0c3dafa4", - "src": "hdca" - } + "json_use|annotation_column": "annotation", + "json_use|db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", + "json_use|execution_enable": true, + "json_use|fragment_column": "fragment", + "json_use|sequence_column": "sequence", + "json_use|table": "sample", + "json_use|use_json_paramers": false }, "job": { - "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmphs5lamwi/files/2/b/e/dataset_2be2db07-173c-45ff-94a0-3461122df268.dat,/tmp/tmphs5lamwi/files/f/1/5/dataset_f1590ccd-1d12-4f95-98b0-fcc4b2cbc80e.dat,/tmp/tmphs5lamwi/files/8/c/2/dataset_8c22a014-8cf2-4575-ae96-c85556a689fb.dat,/tmp/tmphs5lamwi/files/7/f/b/dataset_7fb30eee-10c8-4d84-932e-28f674b1dfc4.dat,/tmp/tmphs5lamwi/files/4/f/b/dataset_4fb6ab60-c194-420f-b10f-de2aa2086638.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmphs5lamwi/job_working_directory/000/13/outputs/dataset_1370843e-a97d-4de9-84c1-8965359a1401.dat' --file_name_mapping '/tmp/tmphs5lamwi/files/2/b/e/dataset_2be2db07-173c-45ff-94a0-3461122df268.dat:p7_L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/f/1/5/dataset_f1590ccd-1d12-4f95-98b0-fcc4b2cbc80e.dat:p6_Nt-IgKLsequence.gb,/tmp/tmphs5lamwi/files/8/c/2/dataset_8c22a014-8cf2-4575-ae96-c85556a689fb.dat:p6_Kozak-ATG.gb,/tmp/tmphs5lamwi/files/7/f/b/dataset_7fb30eee-10c8-4d84-932e-28f674b1dfc4.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/4/f/b/dataset_4fb6ab60-c194-420f-b10f-de2aa2086638.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmphs5lamwi/files/d/0/0/dataset_d00d7320-cfff-4799-af9d-476da677e0c1.dat' --execution_enable 'true'", + "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmp_qydb9xn/files/e/2/4/dataset_e2429fd0-5082-415d-869b-2f7c67516829.dat,/tmp/tmp_qydb9xn/files/8/5/2/dataset_85256206-1030-4b72-bc8d-786951caba8a.dat,/tmp/tmp_qydb9xn/files/d/d/a/dataset_ddae9a40-9b20-4439-8022-532bb18a89a9.dat,/tmp/tmp_qydb9xn/files/1/b/2/dataset_1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f.dat,/tmp/tmp_qydb9xn/files/3/a/9/dataset_3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6.dat' --use_json_paramers 'false' --sequence_column 'sequence' --annotation_column 'annotation' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --execution_enable 'true' --output '/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_c78df7ec-701b-4f3e-8081-d63aa4a4ba90.dat' --file_name_mapping '/tmp/tmp_qydb9xn/files/e/2/4/dataset_e2429fd0-5082-415d-869b-2f7c67516829.dat:p7_L7Ae-Weiss.gb,/tmp/tmp_qydb9xn/files/8/5/2/dataset_85256206-1030-4b72-bc8d-786951caba8a.dat:p6_Nt-IgKLsequence.gb,/tmp/tmp_qydb9xn/files/d/d/a/dataset_ddae9a40-9b20-4439-8022-532bb18a89a9.dat:p6_Kozak-ATG.gb,/tmp/tmp_qydb9xn/files/1/b/2/dataset_1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmp_qydb9xn/files/3/a/9/dataset_3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6.dat:HC_Amp_ccdB.gb' --json_generating 'true' --json_output '/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_705e4a52-0582-42c5-afba-22b1cbe3eb9f.dat' && echo \"DEBUG\" && cat \"/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_705e4a52-0582-42c5-afba-22b1cbe3eb9f.dat\"", "command_version": "", "copied_from_job_id": null, - "create_time": "2025-06-12T08:12:07.955341", + "create_time": "2025-07-11T14:14:15.037467", "dependencies": [ { "cacheable": false, @@ -193,208 +206,36 @@ } ], "exit_code": 0, - "external_id": "126847", - "galaxy_version": "24.2", + "external_id": "133675", + "galaxy_version": "25.0", "handler": null, - "history_id": "8a8d0bbb0c3dafa4", - "id": "e932b28e673f61fd", + "history_id": "6a141869249298e9", + "id": "179da9a21af79ae5", "inputs": { - "adv|json_conf": { - "id": "faf36c8bb3bbf1fc", + "genbank_files1": { + "id": "e058757b81e0ebed", "src": "hda", - "uuid": "d00d7320-cfff-4799-af9d-476da677e0c1" - }, - "genbank_files1": { - "id": "17b31bc27bcedfbf", - "src": "hda", - "uuid": "2be2db07-173c-45ff-94a0-3461122df268" + "uuid": "e2429fd0-5082-415d-869b-2f7c67516829" }, "genbank_files2": { - "id": "5a37da6eaa46c4f4", + "id": "10993b807f8c1a73", "src": "hda", - "uuid": "f1590ccd-1d12-4f95-98b0-fcc4b2cbc80e" + "uuid": "85256206-1030-4b72-bc8d-786951caba8a" }, "genbank_files3": { - "id": "8d24f24cec97882b", + "id": "d964653210776bae", "src": "hda", - "uuid": "8c22a014-8cf2-4575-ae96-c85556a689fb" + "uuid": "ddae9a40-9b20-4439-8022-532bb18a89a9" }, "genbank_files4": { - "id": "07e58d3b99df4277", + "id": "1187622ddb220809", "src": "hda", - "uuid": "7fb30eee-10c8-4d84-932e-28f674b1dfc4" + "uuid": "1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f" }, "genbank_files5": { - "id": "80d24c12e045669e", - "src": "hda", - "uuid": "4fb6ab60-c194-420f-b10f-de2aa2086638" - } - }, - "job_messages": [], - "job_metrics": [], - "job_runner_name": null, - "job_stderr": "", - "job_stdout": "", - "model_class": "Job", - "output_collections": {}, - "outputs": { - "output": { - "id": "e932b28e673f61fd", + "id": "0ec72b924a1ee71e", "src": "hda", - "uuid": "1370843e-a97d-4de9-84c1-8965359a1401" - } - }, - "params": { - "__input_ext": "\"input\"", - "adv": "{\"execution_enable\": true, \"json_conf\": {\"values\": [{\"id\": 12, \"src\": \"hda\"}]}}", - "annotation_column": null, - "chromInfo": "\"/tmp/tmphs5lamwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", - "db_uri": null, - "dbkey": "\"?\"", - "fragment_column": null, - "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}", - "sequence_column": null, - "table": null - }, - "state": "ok", - "stderr": "", - "stdout": "Execution was blocked by config (execution = false)\n", - "tool_id": "seq_to_db", - "tool_stderr": "", - "tool_stdout": "Execution was blocked by config (execution = false)\n", - "update_time": "2025-06-12T08:12:14.967090", - "user_email": "planemo@galaxyproject.org", - "user_id": "d1dc40ebed860870" - }, - "output_problems": [ - "Output output: different than expected\nExpected 5+-0 lines in the output found 0" - ], - "status": "failure", - "test_index": 1, - "time_seconds": 28.067287921905518, - "tool_id": "seq_to_db", - "tool_version": "0.1.0+galaxy0" - }, - "has_data": true, - "id": "seq_to_db-1" - }, - { - "data": { - "inputs": { - "annotation_column": "annotation", - "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", - "fragment_column": "fragment", - "genbank_files": { - "id": "bf0fa404613c4f02", - "src": "hdca" - }, - "sequence_column": "sequence", - "table": "sample" - }, - "job": { - "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmphs5lamwi/files/1/5/a/dataset_15a3a402-8761-43db-81ae-e4bb3f2d41d8.dat,/tmp/tmphs5lamwi/files/0/2/6/dataset_02636863-d06d-46bb-bcd3-c22b162ad92c.dat,/tmp/tmphs5lamwi/files/0/6/a/dataset_06a85205-3621-425b-8eca-56f44a3ceaed.dat,/tmp/tmphs5lamwi/files/5/7/a/dataset_57afe769-fe76-4890-9c62-c2014ecf8529.dat,/tmp/tmphs5lamwi/files/2/a/a/dataset_2aaaf350-bb2f-4390-81e3-6eeeaae0481e.dat' --sequence_column 'sequence' --annotation_column 'annotation' --db_uri 'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db' --table 'sample' --fragment_column 'fragment' --output '/tmp/tmphs5lamwi/job_working_directory/000/19/outputs/dataset_168a000a-8805-4f1d-918e-4ebbd60fd654.dat' --file_name_mapping '/tmp/tmphs5lamwi/files/1/5/a/dataset_15a3a402-8761-43db-81ae-e4bb3f2d41d8.dat:p7_L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/0/2/6/dataset_02636863-d06d-46bb-bcd3-c22b162ad92c.dat:p6_Nt-IgKLsequence.gb,/tmp/tmphs5lamwi/files/0/6/a/dataset_06a85205-3621-425b-8eca-56f44a3ceaed.dat:p6_Kozak-ATG.gb,/tmp/tmphs5lamwi/files/5/7/a/dataset_57afe769-fe76-4890-9c62-c2014ecf8529.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/2/a/a/dataset_2aaaf350-bb2f-4390-81e3-6eeeaae0481e.dat:HC_Amp_ccdB.gb' --json_conf 'None' --execution_enable 'true'", - "command_version": "", - "copied_from_job_id": null, - "create_time": "2025-06-12T08:12:35.708354", - "dependencies": [ - { - "cacheable": false, - "dependency_resolver": { - "auto_init": true, - "auto_install": true, - "can_uninstall_dependencies": true, - "ensure_channels": "conda-forge,bioconda", - "model_class": "CondaDependencyResolver", - "prefix": "/home/rkhaled/miniconda3", - "read_only": false, - "resolver_type": "conda", - "resolves_simple_dependencies": true, - "use_local": false, - "versionless": false - }, - "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", - "exact": true, - "model_class": "MergedCondaDependency", - "name": "pandas", - "version": "2.2.3" - }, - { - "cacheable": false, - "dependency_resolver": { - "auto_init": true, - "auto_install": true, - "can_uninstall_dependencies": true, - "ensure_channels": "conda-forge,bioconda", - "model_class": "CondaDependencyResolver", - "prefix": "/home/rkhaled/miniconda3", - "read_only": false, - "resolver_type": "conda", - "resolves_simple_dependencies": true, - "use_local": false, - "versionless": false - }, - "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", - "exact": true, - "model_class": "MergedCondaDependency", - "name": "sqlalchemy", - "version": "2.0.40" - }, - { - "cacheable": false, - "dependency_resolver": { - "auto_init": true, - "auto_install": true, - "can_uninstall_dependencies": true, - "ensure_channels": "conda-forge,bioconda", - "model_class": "CondaDependencyResolver", - "prefix": "/home/rkhaled/miniconda3", - "read_only": false, - "resolver_type": "conda", - "resolves_simple_dependencies": true, - "use_local": false, - "versionless": false - }, - "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", - "exact": true, - "model_class": "MergedCondaDependency", - "name": "psycopg2", - "version": "2.9.9" - } - ], - "exit_code": 0, - "external_id": "127455", - "galaxy_version": "24.2", - "handler": null, - "history_id": "bf0fa404613c4f02", - "id": "48ac62a10b51b648", - "inputs": { - "genbank_files1": { - "id": "9863db5e96bd9ae2", - "src": "hda", - "uuid": "15a3a402-8761-43db-81ae-e4bb3f2d41d8" - }, - "genbank_files2": { - "id": "c55450b682f38454", - "src": "hda", - "uuid": "02636863-d06d-46bb-bcd3-c22b162ad92c" - }, - "genbank_files3": { - "id": "b2f6887fdac0a65b", - "src": "hda", - "uuid": "06a85205-3621-425b-8eca-56f44a3ceaed" - }, - "genbank_files4": { - "id": "f5829ca36951d902", - "src": "hda", - "uuid": "57afe769-fe76-4890-9c62-c2014ecf8529" - }, - "genbank_files5": { - "id": "baef710e55d31add", - "src": "hda", - "uuid": "2aaaf350-bb2f-4390-81e3-6eeeaae0481e" + "uuid": "3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6" } }, "job_messages": [], @@ -405,222 +246,43 @@ "model_class": "Job", "output_collections": {}, "outputs": { + "json_output": { + "id": "8d85a3e6aa2938f6", + "src": "hda", + "uuid": "705e4a52-0582-42c5-afba-22b1cbe3eb9f" + }, "output": { - "id": "48ac62a10b51b648", + "id": "179da9a21af79ae5", "src": "hda", - "uuid": "168a000a-8805-4f1d-918e-4ebbd60fd654" + "uuid": "c78df7ec-701b-4f3e-8081-d63aa4a4ba90" } }, "params": { "__input_ext": "\"input\"", - "adv": "{\"execution_enable\": true, \"json_conf\": null}", - "annotation_column": "\"annotation\"", - "chromInfo": "\"/tmp/tmphs5lamwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", - "db_uri": "\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\"", + "chromInfo": "\"/tmp/tmp_qydb9xn/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\"", - "fragment_column": "\"fragment\"", - "genbank_files": "{\"values\": [{\"id\": 3, \"src\": \"hdca\"}]}", - "sequence_column": "\"sequence\"", - "table": "\"sample\"" + "genbank_files": "{\"values\": [{\"id\": 2, \"src\": \"hdca\"}]}", + "json_generating": "true", + "json_use": "{\"__current_case__\": 0, \"annotation_column\": \"annotation\", \"db_uri\": \"postgresql://postgres:RK17@localhost:5432/test_fragments_db\", \"execution_enable\": true, \"fragment_column\": \"fragment\", \"sequence_column\": \"sequence\", \"table\": \"sample\", \"use_json_paramers\": false}" }, "state": "ok", "stderr": "", - "stdout": "Connected to database.\nProcessing file: dataset_15a3a402-8761-43db-81ae-e4bb3f2d41d8.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_02636863-d06d-46bb-bcd3-c22b162ad92c.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_06a85205-3621-425b-8eca-56f44a3ceaed.dat(p6_Kozak-ATG)\nProcessing file: dataset_57afe769-fe76-4890-9c62-c2014ecf8529.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_2aaaf350-bb2f-4390-81e3-6eeeaae0481e.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmphs5lamwi/job_working_directory/000/19/outputs/dataset_168a000a-8805-4f1d-918e-4ebbd60fd654.dat'.\n", + "stdout": "JSON configuration written to: /tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_705e4a52-0582-42c5-afba-22b1cbe3eb9f.dat\nConnected to database.\nProcessing file: dataset_e2429fd0-5082-415d-869b-2f7c67516829.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_85256206-1030-4b72-bc8d-786951caba8a.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_ddae9a40-9b20-4439-8022-532bb18a89a9.dat(p6_Kozak-ATG)\nProcessing file: dataset_1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_c78df7ec-701b-4f3e-8081-d63aa4a4ba90.dat'.\nDEBUG\n{\n \"table\": \"sample\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\",\n \"fragment_column\": \"fragment\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"execution\": \"true\"\n}", "tool_id": "seq_to_db", "tool_stderr": "", - "tool_stdout": "Connected to database.\nProcessing file: dataset_15a3a402-8761-43db-81ae-e4bb3f2d41d8.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_02636863-d06d-46bb-bcd3-c22b162ad92c.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_06a85205-3621-425b-8eca-56f44a3ceaed.dat(p6_Kozak-ATG)\nProcessing file: dataset_57afe769-fe76-4890-9c62-c2014ecf8529.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_2aaaf350-bb2f-4390-81e3-6eeeaae0481e.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmphs5lamwi/job_working_directory/000/19/outputs/dataset_168a000a-8805-4f1d-918e-4ebbd60fd654.dat'.\n", - "update_time": "2025-06-12T08:12:41.972140", + "tool_stdout": "JSON configuration written to: /tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_705e4a52-0582-42c5-afba-22b1cbe3eb9f.dat\nConnected to database.\nProcessing file: dataset_e2429fd0-5082-415d-869b-2f7c67516829.dat(p7_L7Ae-Weiss)\nProcessing file: dataset_85256206-1030-4b72-bc8d-786951caba8a.dat(p6_Nt-IgKLsequence)\nProcessing file: dataset_ddae9a40-9b20-4439-8022-532bb18a89a9.dat(p6_Kozak-ATG)\nProcessing file: dataset_1b2fd1a2-9b4f-42f0-a66c-6d7f5b6d935f.dat(p4_Kt-L7Ae-Weiss)\nProcessing file: dataset_3a93ffcc-6958-4761-a4c3-1f6e5b64bbb6.dat(HC_Amp_ccdB)\nInserted 5 fragments.\nFragment names written to '/tmp/tmp_qydb9xn/job_working_directory/000/13/outputs/dataset_c78df7ec-701b-4f3e-8081-d63aa4a4ba90.dat'.\nDEBUG\n{\n \"table\": \"sample\",\n \"sequence_column\": \"sequence\",\n \"annotation_column\": \"annotation\",\n \"fragment_column\": \"fragment\",\n \"db_uri\": \"postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\",\n \"execution\": \"true\"\n}", + "update_time": "2025-07-11T14:14:21.313512", "user_email": "planemo@galaxyproject.org", - "user_id": "d1dc40ebed860870" + "user_id": "5035e3bab9835d6e" }, "status": "success", "test_index": 2, - "time_seconds": 27.17548680305481, + "time_seconds": 26.91756534576416, "tool_id": "seq_to_db", - "tool_version": "0.1.0+galaxy0" + "tool_version": "0.2.0+galaxy1" }, "has_data": true, "id": "seq_to_db-2" - }, - { - "data": { - "inputs": { - "adv|json_conf": { - "id": "81096e298c6cd33b", - "src": "hda" - }, - "genbank_files": { - "id": "f71740853e0eea8f", - "src": "hdca" - } - }, - "job": { - "command_line": "python '/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py' --input '/tmp/tmphs5lamwi/files/7/7/d/dataset_77d5679d-4fb4-4b27-afe7-930f4b3d6076.dat,/tmp/tmphs5lamwi/files/5/1/a/dataset_51ae04ed-e634-4f46-ae13-0ce31dbacc37.dat,/tmp/tmphs5lamwi/files/c/6/4/dataset_c64f9b84-cf82-4b1b-96cb-3f98f0fda7a9.dat,/tmp/tmphs5lamwi/files/e/f/7/dataset_ef7a853c-dc0e-47dc-bf52-6f45291358b1.dat,/tmp/tmphs5lamwi/files/1/3/a/dataset_13a4680c-d654-45d9-bdab-75dca91c36da.dat' --sequence_column '' --annotation_column '' --db_uri '' --table '' --fragment_column '' --output '/tmp/tmphs5lamwi/job_working_directory/000/26/outputs/dataset_431acc98-f2ee-4e32-876a-33ef788c7eeb.dat' --file_name_mapping '/tmp/tmphs5lamwi/files/7/7/d/dataset_77d5679d-4fb4-4b27-afe7-930f4b3d6076.dat:p7_L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/5/1/a/dataset_51ae04ed-e634-4f46-ae13-0ce31dbacc37.dat:p6_Nt-IgKLsequence.gb,/tmp/tmphs5lamwi/files/c/6/4/dataset_c64f9b84-cf82-4b1b-96cb-3f98f0fda7a9.dat:p6_Kozak-ATG.gb,/tmp/tmphs5lamwi/files/e/f/7/dataset_ef7a853c-dc0e-47dc-bf52-6f45291358b1.dat:p4_Kt-L7Ae-Weiss.gb,/tmp/tmphs5lamwi/files/1/3/a/dataset_13a4680c-d654-45d9-bdab-75dca91c36da.dat:HC_Amp_ccdB.gb' --json_conf '/tmp/tmphs5lamwi/files/1/6/8/dataset_1681d2f4-591b-48a4-a469-0b6d9d29897b.dat' --execution_enable 'true'", - "command_version": "", - "copied_from_job_id": null, - "create_time": "2025-06-12T08:13:02.907605", - "dependencies": [ - { - "cacheable": false, - "dependency_resolver": { - "auto_init": true, - "auto_install": true, - "can_uninstall_dependencies": true, - "ensure_channels": "conda-forge,bioconda", - "model_class": "CondaDependencyResolver", - "prefix": "/home/rkhaled/miniconda3", - "read_only": false, - "resolver_type": "conda", - "resolves_simple_dependencies": true, - "use_local": false, - "versionless": false - }, - "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", - "exact": true, - "model_class": "MergedCondaDependency", - "name": "pandas", - "version": "2.2.3" - }, - { - "cacheable": false, - "dependency_resolver": { - "auto_init": true, - "auto_install": true, - "can_uninstall_dependencies": true, - "ensure_channels": "conda-forge,bioconda", - "model_class": "CondaDependencyResolver", - "prefix": "/home/rkhaled/miniconda3", - "read_only": false, - "resolver_type": "conda", - "resolves_simple_dependencies": true, - "use_local": false, - "versionless": false - }, - "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", - "exact": true, - "model_class": "MergedCondaDependency", - "name": "sqlalchemy", - "version": "2.0.40" - }, - { - "cacheable": false, - "dependency_resolver": { - "auto_init": true, - "auto_install": true, - "can_uninstall_dependencies": true, - "ensure_channels": "conda-forge,bioconda", - "model_class": "CondaDependencyResolver", - "prefix": "/home/rkhaled/miniconda3", - "read_only": false, - "resolver_type": "conda", - "resolves_simple_dependencies": true, - "use_local": false, - "versionless": false - }, - "dependency_type": "conda", - "environment_path": "/home/rkhaled/miniconda3/envs/mulled-v1-6494927f0d17ef089d943514f10e32b6b4b401affaea78704675d8f812704966", - "exact": true, - "model_class": "MergedCondaDependency", - "name": "psycopg2", - "version": "2.9.9" - } - ], - "exit_code": 1, - "external_id": "127952", - "galaxy_version": "24.2", - "handler": null, - "history_id": "f71740853e0eea8f", - "id": "ae7479dd630bf125", - "inputs": { - "adv|json_conf": { - "id": "81096e298c6cd33b", - "src": "hda", - "uuid": "1681d2f4-591b-48a4-a469-0b6d9d29897b" - }, - "genbank_files1": { - "id": "4bb85627388cf8ba", - "src": "hda", - "uuid": "77d5679d-4fb4-4b27-afe7-930f4b3d6076" - }, - "genbank_files2": { - "id": "00078d50fa80d7bb", - "src": "hda", - "uuid": "51ae04ed-e634-4f46-ae13-0ce31dbacc37" - }, - "genbank_files3": { - "id": "221d11c5cc4eab13", - "src": "hda", - "uuid": "c64f9b84-cf82-4b1b-96cb-3f98f0fda7a9" - }, - "genbank_files4": { - "id": "bc838ca4b455c7c4", - "src": "hda", - "uuid": "ef7a853c-dc0e-47dc-bf52-6f45291358b1" - }, - "genbank_files5": { - "id": "04052285d124af02", - "src": "hda", - "uuid": "13a4680c-d654-45d9-bdab-75dca91c36da" - } - }, - "job_messages": [ - { - "code_desc": "", - "desc": "Fatal error: Exit code 1 ()", - "error_level": 3, - "exit_code": 1, - "type": "exit_code" - } - ], - "job_metrics": [], - "job_runner_name": null, - "job_stderr": "", - "job_stdout": "", - "model_class": "Job", - "output_collections": {}, - "outputs": { - "output": { - "id": "ae7479dd630bf125", - "src": "hda", - "uuid": "431acc98-f2ee-4e32-876a-33ef788c7eeb" - } - }, - "params": { - "__input_ext": "\"input\"", - "adv": "{\"execution_enable\": true, \"json_conf\": {\"values\": [{\"id\": 25, \"src\": \"hda\"}]}}", - "annotation_column": null, - "chromInfo": "\"/tmp/tmphs5lamwi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\"", - "db_uri": null, - "dbkey": "\"?\"", - "fragment_column": null, - "genbank_files": "{\"values\": [{\"id\": 4, \"src\": \"hdca\"}]}", - "sequence_column": null, - "table": null - }, - "state": "error", - "stderr": "Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 273, in <module>\n main()\n ~~~~^^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 260, in main\n push_gb_annotations(\n ~~~~~~~~~~~~~~~~~~~^\n gb_file_list,\n ^^^^^^^^^^^^^\n ...<6 lines>...\n args.file_name_mapping\n ^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 148, in push_gb_annotations\n raise RuntimeError(f\"Fatal Error: Fragment '{fragment_name}' already exists in DB. Stopping the process.\")\nRuntimeError: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n", - "stdout": "Connected to database.\nProcessing file: dataset_77d5679d-4fb4-4b27-afe7-930f4b3d6076.dat(p7_L7Ae-Weiss)\nError during GB file insertion: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n", - "tool_id": "seq_to_db", - "tool_stderr": "Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 273, in <module>\n main()\n ~~~~^^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 260, in main\n push_gb_annotations(\n ~~~~~~~~~~~~~~~~~~~^\n gb_file_list,\n ^^^^^^^^^^^^^\n ...<6 lines>...\n args.file_name_mapping\n ^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 148, in push_gb_annotations\n raise RuntimeError(f\"Fatal Error: Fragment '{fragment_name}' already exists in DB. Stopping the process.\")\nRuntimeError: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n", - "tool_stdout": "Connected to database.\nProcessing file: dataset_77d5679d-4fb4-4b27-afe7-930f4b3d6076.dat(p7_L7Ae-Weiss)\nError during GB file insertion: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n", - "update_time": "2025-06-12T08:13:09.078361", - "user_email": "planemo@galaxyproject.org", - "user_id": "d1dc40ebed860870" - }, - "output_problems": [ - "Job in error state.. tool_id: seq_to_db, exit_code: 1, stderr: Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 273, in <module>\n main()\n ~~~~^^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 260, in main\n push_gb_annotations(\n ~~~~~~~~~~~~~~~~~~~^\n gb_file_list,\n ^^^^^^^^^^^^^\n ...<6 lines>...\n args.file_name_mapping\n ^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 148, in push_gb_annotations\n raise RuntimeError(f\"Fatal Error: Fragment '{fragment_name}' already exists in DB. Stopping the process.\")\nRuntimeError: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n.", - "Job in error state.. tool_id: seq_to_db, exit_code: 1, stderr: Traceback (most recent call last):\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 273, in <module>\n main()\n ~~~~^^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 260, in main\n push_gb_annotations(\n ~~~~~~~~~~~~~~~~~~~^\n gb_file_list,\n ^^^^^^^^^^^^^\n ...<6 lines>...\n args.file_name_mapping\n ^^^^^^^^^^^^^^^^^^^^^^\n )\n ^\n File \"/home/rkhaled/galaxytools/tools/seq_to_db/save_to_db.py\", line 148, in push_gb_annotations\n raise RuntimeError(f\"Fatal Error: Fragment '{fragment_name}' already exists in DB. Stopping the process.\")\nRuntimeError: Fatal Error: Fragment 'p7_L7Ae-Weiss' already exists in DB. Stopping the process.\n." - ], - "status": "failure", - "test_index": 3, - "time_seconds": 26.706940174102783, - "tool_id": "seq_to_db", - "tool_version": "0.1.0+galaxy0" - }, - "has_data": true, - "id": "seq_to_db-3" } ], "version": "0.1"